This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Selective reaction monitoring (SRM) has the potential to revolutionize the field of proteomics by providing sensitive, specific, reproducible and quantifiable assays for every protein in the proteome. This need is most evident for low abundance proteins such as transcription factors, a class of proteins that bind to and regulate the genome, which are often left undetected by traditional shotgun proteomic approaches. However, the main challenge in targeted proteomics is identifying which peptides and fragment ions should be monitored from a given protein. Consequently, the main goal of this project is to empirically identify for ~550 transcription factors in the human proteome a set of peptides and their fragment ion signatures that can be easily and reproducibly identified from complex mixtures.